Electron microscopic studies of the yeast vacuolar ATPase

The overall structure and subunit arrangement of the yeast V-ATPase were studied by electron microscopy and single-particle image analysis. The cytosolic domain of the V-ATPase, V1, was purified via a FLAG affinity tag fused to the N-terminus of the subunit G. The preparation was active as a Ca-ATPase but not a Mg-ATPase. The two-dimensional top-view electron microscopic projections of the V1 displayed a pseudo-three-fold symmetry with handedness. A three-dimensional electron microscopic model was reconstructed and showed unique knob-like and elongated densities which were assigned to subunit A and the peripheral stator attached to subunit B, respectively. Furthermore, the intact yeast V-ATPase was purified and a three-dimensional electron microscopic model of the entire enzyme was reconstructed. In this model, a striking arc-like structure spans about 270° around the central stalk. Its middle portion is connected with two well resolved peripheral stators and one of its ends forms a handle-like density extending outward. Immunolabeling and difference imaging were employed to localize the position of subunits A, C, G and H. Currently available atomic resolution structures of individual subunits were docked into the three-dimensional model of the yeast V-ATPase. The data show that the knob-like density is a domain of subunit A. At least two copies of subunit G are present in the V-ATPase and they together with subunits E are components of the peripheral stators. Each of subunits C and H occupies an end segment of the arc-like structure. The handle-like density is formed by the N-terminal domain of subunit H. The N-terminal domain of the V0 subunit a is connected to subunit H and it also contributes to the middle section of the arc-like structure. A comparison between the three-dimensional structure of the yeast V-ATPase and those of the isolated yeast V1 and bovine V0 suggests that during V1V0 dissociation, subunit H moves inward to the D/F subcomplex and the N-terminal domain of subunit a bends down towards subunit d. These rearrangements would stop the rotation of the central rotor domain and therefore inhibit MgATPase activity of V1 and proton-pumping function of V0. Preliminary results from crystallization studies of the yeast V1-ATPase are also presented and discussed.